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45 #include "gromacs/legacyheaders/macros.h"
48 #include "gpp_atomtype.h"
50 #include "gromacs/topology/block.h"
51 #include "gromacs/topology/symtab.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/smalloc.h"
57 void set_p_string(t_param *p, const char *s)
61 if (strlen(s) < sizeof(p->s)-1)
63 strncpy(p->s, s, sizeof(p->s));
67 gmx_fatal(FARGS, "Increase MAXSLEN in include/grompp-impl.h to at least %d,"
68 " or shorten your definition of bonds like %s to at most %d",
69 strlen(s)+1, s, MAXSLEN-1);
78 void pr_alloc (int extra, t_params *pr)
82 /* get new space for arrays */
85 gmx_fatal(FARGS, "Trying to make array smaller.\n");
91 assert(!((pr->nr == 0) && (pr->param != NULL)));
92 if (pr->nr+extra > pr->maxnr)
94 pr->maxnr = max(1.2*pr->maxnr, pr->maxnr + extra);
95 srenew(pr->param, pr->maxnr);
96 for (i = pr->nr; (i < pr->maxnr); i++)
98 for (j = 0; (j < MAXATOMLIST); j++)
100 pr->param[i].a[j] = 0;
102 for (j = 0; (j < MAXFORCEPARAM); j++)
104 pr->param[i].c[j] = 0;
106 set_p_string(&(pr->param[i]), "");
111 void init_plist(t_params plist[])
115 for (i = 0; (i < F_NRE); i++)
119 plist[i].param = NULL;
123 plist[i].cmap = NULL;
124 plist[i].grid_spacing = 0;
127 plist[i].cmap_types = NULL;
131 void cp_param(t_param *dest, t_param *src)
135 for (j = 0; (j < MAXATOMLIST); j++)
137 dest->a[j] = src->a[j];
139 for (j = 0; (j < MAXFORCEPARAM); j++)
141 dest->c[j] = src->c[j];
143 strncpy(dest->s, src->s, sizeof(dest->s));
146 void add_param_to_list(t_params *list, t_param *b)
150 /* allocate one position extra */
153 /* fill the arrays */
154 for (j = 0; (j < MAXFORCEPARAM); j++)
156 list->param[list->nr].c[j] = b->c[j];
158 for (j = 0; (j < MAXATOMLIST); j++)
160 list->param[list->nr].a[j] = b->a[j];
162 memset(list->param[list->nr].s, 0, sizeof(list->param[list->nr].s));
168 void init_molinfo(t_molinfo *mol)
171 mol->excl_set = FALSE;
172 mol->bProcessed = FALSE;
173 init_plist(mol->plist);
174 init_block(&mol->cgs);
175 init_block(&mol->mols);
176 init_blocka(&mol->excls);
177 init_atom(&mol->atoms);
182 void done_bt (t_params *pl)
187 void done_mi(t_molinfo *mi)
191 done_atom (&(mi->atoms));
192 done_block(&(mi->cgs));
193 done_block(&(mi->mols));
194 for (i = 0; (i < F_NRE); i++)
196 done_bt(&(mi->plist[i]));
200 /* PRINTING STRUCTURES */
202 void print_bt(FILE *out, directive d, gpp_atomtype_t at,
203 int ftype, int fsubtype, t_params plist[],
206 /* This dihp is a DIRTY patch because the dih-types do not use
207 * all four atoms to determine the type.
209 const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
211 int i, j, f, nral, nrfp;
212 gmx_bool bDih = FALSE, bSwapParity;
214 bt = &(plist[ftype]);
242 case F_CROSS_BOND_ANGLES:
245 case F_CROSS_BOND_BONDS:
295 fprintf(out, "[ %s ]\n", dir2str(d));
299 fprintf (out, "%3s %4s", "ai", "aj");
300 for (j = 2; (j < nral); j++)
302 fprintf (out, " %3c%c", 'a', 'i'+j);
307 for (j = 0; (j < 2); j++)
309 fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
313 fprintf (out, " funct");
314 for (j = 0; (j < nrfp); j++)
316 fprintf (out, " %12c%1d", 'c', j);
320 /* print bondtypes */
321 for (i = 0; (i < bt->nr); i++)
323 bSwapParity = (bt->param[i].C0 == NOTSET) && (bt->param[i].C1 == -1);
326 for (j = 0; (j < nral); j++)
328 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
333 for (j = 0; (j < 2); j++)
335 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
338 fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
340 if (bt->param[i].s[0])
342 fprintf(out, " %s", bt->param[i].s);
346 for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET)); j++)
348 fprintf (out, "%13.6e ", bt->param[i].c[j]);
358 void print_blocka(FILE *out, const char *szName,
359 const char *szIndex, const char *szA,
364 fprintf (out, "; %s\n", szName);
365 fprintf (out, "; %4s %s\n", szIndex, szA);
366 for (i = 0; (i < block->nr); i++)
368 for (i = 0; (i < block->nr); i++)
370 fprintf (out, "%6d", i+1);
371 for (j = block->index[i]; (j < ((int)block->index[i+1])); j++)
373 fprintf (out, "%5d", block->a[j]+1);
381 void print_excl(FILE *out, int natoms, t_excls excls[])
388 for (i = 0; i < natoms && !have_excl; i++)
390 have_excl = (excls[i].nr > 0);
395 fprintf (out, "[ %s ]\n", dir2str(d_exclusions));
396 fprintf (out, "; %4s %s\n", "i", "excluded from i");
397 for (i = 0; i < natoms; i++)
401 fprintf (out, "%6d ", i+1);
402 for (j = 0; j < excls[i].nr; j++)
404 fprintf (out, " %5d", excls[i].e[j]+1);
414 static double get_residue_charge(const t_atoms *atoms, int at)
419 ri = atoms->atom[at].resind;
421 while (at < atoms->nr && atoms->atom[at].resind == ri)
423 q += atoms->atom[at].q;
430 void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
431 gmx_bool bRTPresname)
439 as = dir2str(d_atoms);
440 fprintf(out, "[ %s ]\n", as);
441 fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
442 "nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
448 fprintf(debug, "This molecule has %d atoms and %d residues\n",
454 /* if the information is present... */
455 for (i = 0; (i < at->nr); i++)
457 ri = at->atom[i].resind;
458 if ((i == 0 || ri != at->atom[i-1].resind) &&
459 at->resinfo[ri].rtp != NULL)
461 qres = get_residue_charge(at, i);
462 fprintf(out, "; residue %3d %-3s rtp %-4s q ",
464 *at->resinfo[ri].name,
465 *at->resinfo[ri].rtp);
466 if (fabs(qres) < 0.001)
468 fprintf(out, " %s", "0.0");
472 fprintf(out, "%+3.1f", qres);
476 tpA = at->atom[i].type;
477 if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
479 gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
482 fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
487 *(at->resinfo[at->atom[i].resind].rtp) :
488 *(at->resinfo[at->atom[i].resind].name),
489 *(at->atomname[i]), cgnr[i],
490 at->atom[i].q, at->atom[i].m);
491 if (PERTURBED(at->atom[i]))
493 tpB = at->atom[i].typeB;
494 if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
496 gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
498 fprintf(out, " %6s %10g %10g",
499 tpnmB, at->atom[i].qB, at->atom[i].mB);
501 qtot += (double)at->atom[i].q;
502 if (fabs(qtot) < 4*GMX_REAL_EPS)
506 fprintf(out, " ; qtot %.4g\n", qtot);
513 void print_bondeds(FILE *out, int natoms, directive d,
514 int ftype, int fsubtype, t_params plist[])
517 gpp_atomtype_t atype;
522 atype = init_atomtype();
526 for (i = 0; (i < natoms); i++)
529 sprintf(buf, "%4d", (i+1));
530 add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
532 print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
537 done_atomtype(atype);